Take a good look at your character's powers and ask yourself which source would make the most sense for them - or, if you're already considering one particular source, whether that source actually makes sense, or whether something else would work better.
Let's say you wanted your character to have control over the four classical elements (earth, air, fire, and water), and you're operating in a universe that's shown to generally behave in a naturalistic manner (ie, without supernatural forces behind the workings of the universe).
To explain where these powers come from, you give your character a genetic mutation. But - one little snag here: by choosing mutation as the source of your character's powers, they are in source biological, and therefore naturalistic. In the natural world, the four classical elements are vastly different things that chemically and energetically don't relate to each other as much to other things. For example, since fire's a plasma, it has more in common with electricity than water. Water, by virtue of having two hydrogen atoms, has more in common with vinyl than it does with Earth's atmosphere (which does have some hydrogen in it, but the amount is so small that it makes up less than one percent of the atmosphere).
If you want to write it off as that your character can control four states of matter (solid, liquid, gas, and plasma), then there is very little in the universe your character would logically be unable to control, since pretty much everything is in one of these states.
To make an artistic comparison, this is a little like making your character able to control primary colors, but nothing in between. Why can your character control blue and yellow, but not green when green is just a blend of blue and yellow? If your character's powers come from a magic color fairy who has the power to say which colors your character can and cannot control, sure, it makes sense. It can also make sense if your world is one that operates on fundamentally different principles than the real world does (see: Rainbow Brite).
The four classical elements, being a philosophical and/or mystical concept, make sense if the world itself operates on mystical principles (ala Avatar: The Last Airbender), or if the character has a magical, supernatural, or divine source of power, or if your character was in a comic book-style lab accident where xe was specifically exposed to earth, air, fire, and water. But if your character's supposed to be from a naturalistic world that operates more or less like the real world, and if xir powers come from a random mutation, fridge logic will follow your character everywhere.
On the other hand, there's no indication in Avatar: The Last Airbender that you can get powers through mutations or gamma rays, and such a thing wouldn't fit the tone of the universe too well.
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